Despite the introduction of highly active antiretroviral treatment (HAART), the prevalence of HIV-associated neurocognitive disorders (HAND) among HIV-1-infected patients has increased. Currently, there is no effective therapy for HAND; therefore, a better understanding of the viral evolutionary factors driving the emergence of neurovirulent strains during disease onset and progression is of pivotal importance for developing a mechanistic model of neuroAIDS and improvement of drug design strategies. The objectives of the current proposal are to identify and characterize spatiotemporal dynamics of viral evolution among peripheral and central nervous system (CNS) tissues and cell populations associated with the onset and progression of neuropathogenesis in two distinct rhesus macaque models of neuroAIDS. Eighteen total macaques were infected with a genetically characterized viral swarm, from which peripheral blood and tissue samples were collected over time and used for amplification of viral gp120 genomic RNA. High-resolution phylogeographic analyses will reveal spatial and temporal aspects of intra-host viral seeding of the brain linked to the onset of a neuropathogenic infection that have not yet been characterized because of ethical issues associated with tissue sampling in humans. Specific Aim 1 will investigate the migration (gene flow) of cell-free virus from plasma and cell-associated virus from lymphoid tissues and peripheral blood mononuclear cells (PBMCs) to the CNS during the course of infection via longitudinal PBMC/tissue sampling and brain biopsies of macaques with and without CD8+ lymphocyte depletion. Specific Aim 2 will measure biomarkers of encephalitis-associated brain injury over time in order to investigate the link between viral evolutionary and population dynamics observed in Specific Aim 1 and disease onset and progression. Ultimately, we will be able to identify the spatiotemporal patterns of brain infection and evolutionary signatures leading to the emergence of neurotropic and neurovirulent populations that could be used to predict and monitor disease progression. Equally important is the potential utilization of these findings in th development of drugs that target viral and/or infected immune cell populations associated with neuropathogenesis. Overall, we will undertake the most comprehensive analysis of longitudinal SIV sequences from a variety of tissues to date. The principle investigator associated with this project, Dr. Marco Salemi, has significant experience in phylogenetic analysis and has worked to cultivate a resource-rich environment critical for the success of this project as well as my pre doctoral career. In addition, we have assembled a unique and qualified interdisciplinary advisory committee to assist in oversight and progression of this study.